Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
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Accurate, conformation-dependent predictions of solvent effects on protein ionization constantsBlind Prediction of Charged Ligand Binding Affinities in a Model Binding Site300-Fold Increase in Production of the Zn2+-Dependent Dechlorinase TrzN in Soluble Form via Apoenzyme StabilizationDivalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia colipH replica-exchange method based on discrete protonation statesComputational protein design: the Proteus software and selected applications.Proton binding to proteins: a free-energy component analysis using a dielectric continuum model.Factors influencing the energetics of electron and proton transfers in proteins. What can be learned from calculations.Is arginine charged in a membrane?pKa of residue 66 in Staphylococal nuclease. I. Insights from QM/MM simulations with conventional sampling.Dielectric relaxation of cytochrome c oxidase: Comparison of the microscopic and continuum models.Modeling and simulation of ion channels.Stabilization of internal charges in a protein: water penetration or conformational change?Effects of Restrained Sampling Space and Nonplanar Amino Groups on Free-Energy Predictions for RNA with Imino and Sheared Tandem GA Base Pairs Flanked by GC, CG, iGiC or iCiG Base PairsConstant pH replica exchange molecular dynamics in biomolecules using a discrete protonation modelRole of Lys-12 in catalysis by triosephosphate isomerase: a two-part substrate approach.Protonation/deprotonation effects on the stability of the Trp-cage miniprotein.Chemical versus mechanical perturbations on the protonation state of arginine in complex lipid membranes: insights from microscopic pKa calculationsAn accurate density functional theory based estimation of pK(a) values of polar residues combined with experimental data: from amino acids to minimal proteins.Bluues: a program for the analysis of the electrostatic properties of proteins based on generalized Born radii.Constant pH molecular dynamics with proton tautomerism.Depth: a web server to compute depth, cavity sizes, detect potential small-molecule ligand-binding cavities and predict the pKa of ionizable residues in proteins.Deciphering the role of glucosamine-6-phosphate in the riboswitch action of glmS ribozymeSubunit-subunit interactions are critical for proton sensitivity of ROMK: evidence in support of an intermolecular gating mechanismParameterization of highly charged metal ions using the 12-6-4 LJ-type nonbonded model in explicit water.On the role of electrostatics in protein-protein interactions.Electrostatic potential energy within a protein monitored by metal charge-dependent hydrogen exchangeA conserved asparagine residue in transmembrane segment 1 (TM1) of serotonin transporter dictates chloride-coupled neurotransmitter transportComputing Alchemical Free Energy Differences with Hamiltonian Replica Exchange Molecular Dynamics (H-REMD) Simulations.Conformational relaxation and water penetration coupled to ionization of internal groups in proteins.Rapid calculation of protein pKa values using Rosetta.Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH.Does arginine remain protonated in the lipid membrane? Insights from microscopic pKa calculations.High-throughput pKa screening and prediction amenable for ADME profiling.Developing polarized protein-specific charges for protein dynamics: MD free energy calculation of pKa shifts for Asp26/Asp20 in thioredoxinSingle-ion solvation free energies and the normal hydrogen electrode potential in methanol, acetonitrile, and dimethyl sulfoxide.Adding explicit solvent molecules to continuum solvent calculations for the calculation of aqueous acid dissociation constants.Rational Design of Particle Mesh Ewald Compatible Lennard-Jones Parameters for +2 Metal Cations in Explicit Solvent.Mechanism of activation of elongation factor Tu by ribosome: catalytic histidine activates GTP by protonation.Progress in ab initio QM/MM free-energy simulations of electrostatic energies in proteins: accelerated QM/MM studies of pKa, redox reactions and solvation free energies
P2860
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P2860
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
description
2004 nî lūn-bûn
@nan
2004 թուականի Ապրիլին հրատարակուած գիտական յօդուած
@hyw
2004 թվականի ապրիլին հրատարակված գիտական հոդված
@hy
2004年の論文
@ja
2004年論文
@yue
2004年論文
@zh-hant
2004年論文
@zh-hk
2004年論文
@zh-mo
2004年論文
@zh-tw
2004年论文
@wuu
name
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@ast
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@en
type
label
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@ast
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@en
prefLabel
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@ast
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@en
P356
P1476
Proton binding to proteins: pK(a) calculations with explicit and implicit solvent models.
@en
P2093
David A Case
P304
P356
10.1021/JA039788M
P407
P577
2004-04-01T00:00:00Z